Chapter 10 Gut microbiota: functional analysis
10.1 MCI
GIFTs_functions_community %>%
rowMeans() %>%
as_tibble(., rownames = "sample") %>%
left_join(sample_metadata, by = join_by(sample == sample)) %>%
# filter(time_point=="0_Wild") %>%
group_by(environment) %>%
summarise(MCI = mean(value), sd = sd(value))# A tibble: 2 × 3
environment MCI sd
<fct> <dbl> <dbl>
1 low 0.321 0.0149
2 high 0.298 0.0288MCI <- GIFTs_functions_community %>%
rowMeans() %>%
as_tibble(., rownames = "sample") %>%
left_join(sample_metadata, by = join_by(sample == sample))
# %>%
# filter(diet!="Post_grass")
shapiro.test(MCI$value)
Shapiro-Wilk normality test
data: MCI$value
W = 0.78617, p-value = 3.708e-05
Wilcoxon rank sum exact test
data: value by environment
W = 184, p-value = 0.002306
alternative hypothesis: true location shift is not equal to 0
10.2 Wilcoxon
10.2.1 Community elements differences:
Elements low high Function
1 B0205 0.6215078000 0.556359700 Amino acid biosynthesis_Threonine
2 B0208 0.7210440000 0.636853500 Amino acid biosynthesis_Valine
3 B0211 0.7945017000 0.725047800 Amino acid biosynthesis_Lysine
4 B0212 0.6037965000 0.534577500 Amino acid biosynthesis_Arginine
5 B0216 0.5185759000 0.403716800 Amino acid biosynthesis_Tryptophan
6 B0217 0.4350579000 0.386313200 Amino acid biosynthesis_Phenylalanine
7 B0303 0.2366397000 0.210934100 Amino acid derivative biosynthesis_Ectoine
8 B0309 0.0982039000 0.080454810 Amino acid derivative biosynthesis_Putrescine
9 B0310 0.0074509910 0.001588408 Amino acid derivative biosynthesis_Tryptamine
10 B0403 0.5460416000 0.526315000 SCFA biosynthesis_Propionate
11 B0602 0.7980851000 0.748664900 Organic anion biosynthesis_Fumarate
12 B0710 0.1077906000 0.069865730 Vitamin biosynthesis_Phylloquinone (K1)
13 B0805 0.2209180000 0.163027300 Aromatic compound biosynthesis_Indole-3-acetate
14 B1014 0.0002108536 0.002070099 Antibiotic biosynthesis_Kanosamine
15 D0104 0.1621682000 0.121988700 Lipid degradation_Dicarboxylic acids
16 D0204 0.4792235000 0.412658000 Polysaccharide degradation_Chitin
17 D0206 0.5883225000 0.484839300 Polysaccharide degradation_Alpha galactan
18 D0210 0.3375139000 0.277216900 Polysaccharide degradation_Beta-mannan
19 D0213 0.3703334000 0.300628500 Polysaccharide degradation_Mucin
20 D0302 0.1295141100 0.087387210 Sugar degradation_Sucrose
21 D0310 0.4599834000 0.385078900 Sugar degradation_NeuAc
22 D0603 0.0174939660 0.004478505 Nitrogen compound degradation_Urate
23 D0606 0.0327311000 0.019533340 Nitrogen compound degradation_Allantoin
24 D0704 0.4279568000 0.338026300 Alcohol degradation_Glycerol
25 D0807 0.0550681500 0.028201350 Xenobiotic degradation_Catechol
26 D0816 0.1240800200 0.098151990 Xenobiotic degradation_Phenylacetate
27 D0817 0.0139664790 0.008498965 Xenobiotic degradation_Trans-cinnamate
28 S0104 0.2384995000 0.206859100 Cellular structure_Lipoteichoic acid
